Gut Dysbiosis Sets the Stage for Diseases of Civilization

inner-dwellersMany of the chronic health disorders – such as inflammatory bowel diseases, acne vulgaris, and type-2 diabetes – that now affect a growing part of the population in the modern world are virtually absent in hunter-gatherer populations and other traditional, non-westernized cultures. These differences in disease burden are primarily a result of a modern lifestyle that is at odds with our ancient genome (1, 2). Inactivity, poor nutrition, inadequate sun exposure, disorganized circadian rhythms, excessive hygiene/inadequate microbial exposure, exposure to hazardous chemicals, and chronic stress seem to be the key lifestyle factors that drive the high rates of many chronic mismatch diseases in the western world today (1, 2). It’s been known for a long time that these types of stimuli negatively impact your health by influencing how your genes are expressed, but what we’ve learned over the last couple of years is that the impact on our second genome – the Human Microbiome – is in some ways even more severe.

As I explained in my previous post on microbes, my interest in the human microbiome began because I was wrapping my mind around things that weren’t explained using the conventional approach to health/medicine. Simply looking at the human body as a singular organism got me nowhere. When I first started reading up on microbiome about 6-7 years ago, there wasn’t really a lot of information to go on. The research in the area was still in the very early stages, and only a small minority even believed that conditions such as “leaky gut“, candida overgrowth, and dysbiosis existed. However, much has changed over the years. Although there’s still a lot we don’t know about the critters that live in and on our bodies, it has become abundantly clear that the microbiome has a profound impact on our health…

Contrary to the human genome we carry with us throughout life, the microbiome is a dynamic and adaptable community of trillions of microorganisms that inhabit our skin, lungs, digestive tract, and several other locations on our body. Microbial cells greatly outnumber our human cells and provide essential functions that we can’t do without.

The gut microbiota is often labelled as the “forgotten organ”, as it’s only recently we’ve really started to understand how essential the trillions of microbes living in our gut are to our health. However, what we have to remember is that although the human body can be considered a superorganism, these microbes aren’t really “us”. They are very much a part of our environment, and in that regard, an essential part of the gene-environment mismatch I talk so much about on this site. To understand this, let’s start with a little history of our co-evolution with bacteria, viruses, fungi, and archaea.

Symbiotic relationships between multicellular organisms and microbes were forged millions of years ago

We can easily imagine part of the reason this symbiotic relationship between multicellular organisms and microbes came to be. As microorganisms aid in digesting otherwise indigestible food components and help in the protection against pathogens, working with bacteria provide a major survival advantage for multicellular eukaryotic organisms. Instead of going through the slow biological evolution of developing our own means of digesting non-starch polysaccharides, we outsourced the job to microbes. As for pathogen resistance, we don’t have to look further than the increasing prevalence of C. difficile infection to understand that our commensal microbes are absolutely essential to us. In return for their services, we (the host) provide them with food and “shelter”; forging a symbiotic relationship.

Survival and reproduction are the basis for evolution, and the only way a symbiotic relationship like this could evolve is if both partners benefit in some way.

The host benefits because it has outsourced certain aspects of its digestive function, metabolism, and immunity to microorganisms. Without microbes, the host can’t function properly.
Gut microbes benefit because the host provides an environment where they can live. They get energy through the host’s diet and from certain compounds produced in the gut lining.

Man and microbe march on

It’s widely believed that when meat started becoming an increasingly important part of the hominin diet about 2.6 million years ago, our digestive systems started to change. Perhaps most importantly, our large intestines got smaller as a result of transitioning from a diet primarily made up of low quality plant foods to a diet of higher quality. In other words, we no longer had the same need for microbial fermentation, as more of our food was broken down by host enzymes and absorbed in the small intestine. However, we didn’t completely cut the bonds with our microbial inhabitants. Far from it.

Root vegetables, fruits, and other fibrous foods were an important part of the diet for many paleolithic tribes, and the job of breaking down the indigestible (to the human host) compounds in these foods were allocated to the microbial reactor deep in our guts.

So, when we lived as hunter-gatherers on the African savanna, we probably supplied the microorganisms in our guts with plenty of food through the diet we were taking in. This idea is supported by studies of contemporary hunter-gatherers – such as the Hadza – who often (not always) consume large amounts of dietary fiber every day (3, 4). Besides supplying bacteria with fermentable substrates, hunter-gatherers routinely pick up new microorganisms from dirty food, soil, and the rest of the natural environment

Man and microbe collide with a modern lifestyle

So, what happened? Major changes to the human microbiome probably started occurring with the agricultural revolution, as we started to settle down and incorporate new foods into our diet (5, 6, 7). As we know, this transition (at least at first) caused a decline in human health; much of which was due to infectious mismatch diseases that started to run rampant as a result of unsanitary living conditions, but also due to other lifestyle changes, such as the transition to eating a starchy, less nutritious diet.

All of this would certainly have affected our microbial inhabitants, as our new lifestyle exposed us to novel microorganisms and selected for a different microbiome composition.

However, the changes that occurred with the neolithic revolution is nothing compared to what has happened over the last several centuries – and especially the last couple of decades. Let’s take a look at some of the characteristics of life in the modern, western world:

  • We’ve disconnected ourselves from the natural environment by moving into large apartment buildings.
  • We’ve overused antibiotics.
  • We’ve started eating diets that don’t resemble anything our prehistoric ancestors ate. E.g., highly refined, high in grains/starch.
  • We’ve disrupted our circadian rhythm.
  • We’ve become “obsessed” with cleanliness.
  • We exercise less and spend little time outdoors.
  • We’ve created a “clean” food supply.

The evidence showing that this orchestra promote a disrupted microbiome is overwhelming (e.g., 5, 6, 7, 8, 9, 10).

As a result of these changes, two things have occurred:
We’ve lost many microorganisms that used to be a part of the human microbiome
We’ve selected for a microbiome that is very different from that of our prehistoric ancestors

Suddenly, our inner environment has changed dramatically. For millions of years we carried a diverse microbiota dominated by organisms that we evolved to live in mutualistic symbiosis with, but now we have suddenly disrupted this equilibrium in a profound way. By eating novel foods we’re selecting for the growth of microbes in the gut that never used to make up a large part of the ancestral microbiome, and through the use of antibiotics we’re losing microbial old friends – essentially wiping out part of the community structure.

No wonder we’re seeing such a rapid rise in IBS, IBD, food intolerance, and other gut-related disorders. That’s not to say microbial imbalance is the only cause of these conditions; of course not, but it’s definitely an important one (11, 12). And, as we know, the havoc doesn’t stop there. Gut dysbiosis has far-reaching effects and has been linked to many chronic diseases that don’t directly involve the gut.

We’ve changed our environment too rapidly for our bodies to keep pace, and now we’re suffering the consequences.

Dealing with the problem

For many, gut microbiota restoration is synonymous with yogurt and probiotic supplements, which typically contain a couple of strains of lactic acid bacteria. However, for those of us who us who look at health & fitness through the lens of evolution, the downfalls of this approach quickly become evident. First of all, the human gut consists of hundreds of species of microorganisms, and while dairy probiotics could contribute some genes to bacteria living in biofilms, they clearly don’t restore a healthy, diverse gut microbiome. Second, bacteria found in yoghurt are primarily adapted to live in yoghurt – not in the human gut.

That’s not to say these bugs don’t provide any value (research has shown that they do), but the benefits are limited.

Through our evolution we didn’t acquire microbes from fermented dairy, but rather from mum, other people, animals, water, and soil/dirt.

So, what should we do? We don’t have all the answers and solutions yet, but here’s my general thoughts…

– For those with no apparent gut-related conditions and/or mild dysbiosis, adopting a more paleo-based lifestyle should be enough to achieve very good health. Most importantly, eat a diet rich in fermentable substrates and fermented foods and supplement with some high-quality probiotics.

– For those with more severe dysbiosis; lifestyle changes, including probiotics, prebiotics, and dietary changes, is definitely an important part of the healing process. However, it’s probably often not going to be enough. A healthy gut microbiota is composed of hundreds of species of microorganisms, a diversity that can be hard to come by through food and supplements (at least those available today).

Of course, the ultimate probiotic is bacteria extracted from the feces of a healthy donor, and several studies have shown a cure rate of approximately 90% when treating C. difficile patients with fecal microbiota transplantations (FMTs) (13). Research looking into the effects of this treatment in other conditions are still in the early stages, and when they are published they will give us many answers as to how valuable this treatment really is. One of the greatest challenges with FMT is to find good donors; as pretty much everyone in the world today have taken antibiotics, eaten refined diets, etc.

For those that are “grossed” our by the whole poop thing, other alternatives are on the horizon. Several biotech companies are now in the process of developing advanced probiotics/microbiome modulators that might be effective solutions for treating dysbiosis (14).

Sadly, the conventional medical community are often more concerned with treating symptoms than root causes, and diet, exercise, and other lifestyle factors that have a profound impact on health and longevity are barely covered in medical schools. As for gut dysbiosis, simple and effective solutions to this condition are still very hard to come by through conventional medical channels, but there’s hope in the horizon…


  1. wow you just dropped a bomb……not the smelly kind 🙂 The last point you bring up is a great one. Exercise and food are the greatest tools we have in healing ourselves.

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